MOTIVATION: A ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To accomplish this task numerous software tools have been proposed. Determining the mappers that are most suitable for a specific application is not trivial. RESULTS: This survey focuses on classifying mappers through a wide number of characteristics. The goal is to allow practitioners to compare the mappers more easily and find those that are most suitable for their specific problem. AVAILABILITY: A regularly updated compendium of mappers can be found at http://wwwdev.ebi.ac.uk/fg/hts_mappers/http://wwwdev.ebi.ac.uk/fg/hts_mappers/. CONTACT: nf@ebi.ac.uk SUPPLEMENTARY INFORMATION: Supplementary information on this manuscript is available online.